In jianhong/deepToolsDownstream: downstream plots for deepTools

suppressPackageStartupMessages({
  library(deepToolsDownstream)
  library(SummarizedExperiment)
  library(S4Vectors)
  library(colorBlindness)
  library(ggplot2)
})
knitr::opts_chunk$set(warning=FALSE, message=FALSE)

Quick start

library(deepToolsDownstream)
file <- system.file("extdata", "count.gz", package= "deepToolsDownstream")
## step 1 import file
se <- importCount(file)
## step 2 plots
## plot profile
p <- plotProfile(se)
library(S4Vectors)
library(colorBlindness)
library(ggplot2)
cols <- safeColors[-1][seq_along(metadata(se)$sample_labels)]
names(cols) <- metadata(se)$sample_labels
plot(p + scale_color_manual(values = cols))
## plot heatmap
plotHeatmap(se, 
            fill_gradient = 
              scale_fill_gradient2(
                low = "darkblue", mid = "yellow",
                high = "red", midpoint = 3.5),
            yaxis_breaks="100033817", #The position to highlight
            yaxis_label="geneA") # the lable to highlight
## subset data
library(SummarizedExperiment)
keep <- rowMeans(assays(se)[[1]], na.rm = TRUE) < 2 ## arbitory number
nrow(se)
se <- filterCount(se, subset=keep)
nrow(se)
table(keep)
## export data as matrix data for deepTools to plot
exportCount(se, file=tempfile())

jianhong/deepToolsDownstream documentation built on Oct. 22, 2021, 7:48 a.m.